Experience

• Developed cryoWEight, a maximum-entropy reweighting framework that biases molecular dynamics ensembles toward cryo-electron microscopy distributions to recover experimentally validated conformational landscapes and kinetics.
• Developed ManifoldEM, a geometric machine-learning approach to infer reaction coordinates and free-energy landscapes directly from single-particle cryo-electron microscopy images without prior structural models.
• Developed seekrflow, a fully automated multiscale milestoning pipeline integrating machine-learned force fields and enhanced sampling for high-throughput prediction of drug-target residence times, binding kinetics, and free energies.
• Designed stable hinge proteins with conformational switching for therapeutic applications using multiscale simulations.

• Developed a thermodynamic-kinetic metric using deep learning and multiscale kinetics to predict PROTAC permeability and residence times in quaternary complexes across multiple solvents.
• Improved binding-kinetics predictions for kinase targets via multiscale simulations, accelerating residence-time-driven hit-to-lead optimization across multiple therapeutic targets.

• Developed AI-enhanced multiscale molecular and Brownian dynamics simulations to estimate protein-protein kinetics.
• Developed an end-to-end computational workflow to streamline multiscale simulations for kinetic pathway modeling.

• Employed deep learning and enhanced sampling to determine permeability and rank ordering of protein degraders.
• Developed an end-to-end Python workflow for blind permeability predictions of beyond-rule-of-five protein degraders.

• Employed MSM and enhanced sampling to estimate transition rates of protein degraders between metastable states.
• Developed an end-to-end Python framework to generate customizable force field parameters for protein degraders.

Published 12 research publications with 7 first-author publications showcasing distinctive scientific understanding.

• Developed milestoning simulations with dissipation-corrected targeted MD to estimate accurate drug-target residence times.
• Developed seekr, a multiscale milestoning software with Voronoi tessellations, enabling 10-fold faster drug-target (un)binding kinetics predictions across multiple therapeutic targets for accelerated drug discovery campaigns.
• Developed QMrebind, a QM-MM reparameterization tool for accurate and efficient drug-residence time estimates via multiscale milestoning.
• Developed GaMD-WE, a hybrid GaMD and weighted ensemble simulation protocol for 2-fold faster sampling of biomolecular kinetics and thermodynamics.
• Developed DeepWEST, combining deep learning, MSMs, and WE simulations for improved biomolecular kinetics.
• Employed chemoinformatics and machine learning to identify 8 physicochemical properties differentiating OATP- and OAT-transported drugs for informed drug selection.

• Elucidated JAK2/JAK3 inhibitor selectivity and rank-ordered 8 inhibitors by residence time via multiscale milestoning.
• Investigated allosteric effects of 5 disease-associated LRRK2 mutations using GaMD and WE simulations for therapeutic insights.
• Identified SARS-CoV-2 spike protein stabilizing mutations via WE simulations for improved immunogen design.

• Conducted ab-initio electronic structure calculations (Density Functional Theory and Hartree-Fock) in ORCA simulation engine to characterize colorimetric chemosensor to determine copper selectivity.

• Developed a Python workflow to compute concerted hydrogen transfer rates in water clusters (3-10 molecules) using ring-polymer instanton theory.

• Performed ab-initio calculations in Gaussian to estimate binding free energies and rank-order analytes interacting with MOFs.
• Employed DFT calculations in VASP to compute interaction energies of glyphosate molecules with zirconium-based MOFs.

• Performed hybrid-functional DFT and nudged elastic band calculations in Quantum ESPRESSO to compute activation-energy barriers for hydrogen diffusion on noble-metal surfaces.
• Performed molecular dynamics and adsorption simulations to calculate alkane binding energies on metal surfaces.

• Performed QM/MM MD simulations in NAMD to elucidate substrate binding and the catalytic mechanism of DapE with transition-metal centers.

• Employed DFT and HF calculations in Gaussian to investigate quantum tunneling phenomena in N-heterocyclic carbenes.
• Employed QM calculations in Gaussian and ORCA to quantify cyclooctatetraene interactions on noble metal surfaces.